The mystery of the alien egg catacombs beneath the crashed Mala'kak ship remain an enigma. Many theories abound.
I don't think the catacombs are a part of the Mala'kak derelict as the scale appears to far exceed that of the ship. It does appear to be of Mala'kak design and construct and not that of the Engineers.

We may never know what the Mala'kak pilot's mission was. It is likely that it knew it was infested with an Xenomorph embryo due to being a part of the ship and it would make sense for its biology to be continuously monitored. It would be trying to make it to a Mala'kak facility before a medical emergency occurs, but it fails.
In Alien, Aliens and the Alien Isolation game, there's no mention of any other structures apart from the Derelict ship and the human colony of Hadley's Hope. In Aliens, the Derelict is only re-discovered due to Carter's intervention. There's no real indication that an extensive survey was made of LV-426. The Derelict is large and unless its structural material doesn't show up on the scans, this supports that no extensive survey was conducted.
Further, we have H.R. Giger's original concept art for Alien where the Derelict wasn't a ship but a temple or pyramid.

We know a Xenomorph Chestburster erupted from the Mala'kak pilot. But we never know what it looks like or what its capabilities are. It would be awesome to see this explored with the Mala'kak species. I suspect it would be considered an abomination and to be destroyed as a high priority. Could it possibly be the source of the Xenomorph Queen?
Supporting this idea is the size and shape of the Queen and the differences between it and the other Xenomorphs. We also see the acid burn hole in the floor of the Derelict command centre. Unlike all the acid melt holes we have seen since, this one is quite a neat square shape that follows the contours of the floor panel - unlike the round shaped holes we see later in Alien, Aliens and Alien Romulus.

If the facility already had Xenomorph eggs prior to the Mala'kak ship crashing on LV-426, it is possible that the Mala'kak Xenomorph could sense these and deliberately injure itself in order to create its own path to the chamber below. Another possibility is that the Mala'kak Xenomorph could just sense, via it's merged Mala'kak DNA, that the closest part of the Mala'kak structure is below. If it does and the chambers are empty, and it is a Queen, then it could explain all the eggs.
Again, it would be fun to see some explanation or exploration of this fascinating location.